An eXtracted Ion Chromatogram (XIC). More...

#include <ms_xic.hpp>

Inherits matrix_science::ms_handle.

Public Types
enum	peakState { PEAK_STATE_UNKNOWN = 0, PEAK_STATE_OK = 1, PEAK_STATE_DISCARD = 3 }
	Status codes from fitting peaks. More...
Public Member Functions
	ms_xic ()
	Default constructor.
	ms_xic (const ms_xic_body &body)
	Populated constructor. Performs a deep copy of the passed object.
	ms_xic (ms_xic_body *body)
	Constructor that use the same pointer as passed.
void	copyFrom (const ms_xic *src)
	Perform a deep copy of the contents.
void	defaultValues ()
	Use this member to re-initialise internal members.
double	getElutionTimeShift () const
	Get the elution time shift in seconds.
int	getEndIndex () const
	Get the end index. Only valid if the XIC was processed separately.
int	getEndScanId () const
	Get the id of the end scan.
int	getNumPoints () const
	Get the number of points.
int	getPeakEndIndex () const
	Get the end of the peak. Only valid if the XIC was processed separately.
int	getPeakEndScanId () const
	Get the index of the peak end.
int	getPeakStartIndex () const
	Get the start of the peak. Only valid if the XIC was processed separately.
int	getPeakStartScanId () const
	Get the index of the peak start.
peakState	getPeakState () const
	Get the state of the peak.
void	getPoint (int index, double &rt, int &scanId, double &intensity) const
	Get a point's values; retention time, scan number and intensity (index 1..n).
int	getRegionEndIndex () const
	Get the end of the region. Only valid if the XIC was processed separately.
int	getRegionEndScanId () const
	Get the index of the region end.
int	getRegionStartIndex () const
	Get the start of the region. Only valid if the XIC was processed separately.
int	getRegionStartScanId () const
	Get the index of the region start.
double	getRtPeakEnd () const
	Get the retention time of the peak end.
double	getRtPeakStart () const
	Get the retention time of the peak start.
double	getRtRegionEnd () const
	Get the retention time of the region end.
double	getRtRegionStart () const
	Get the retention time of the region start.
int	getStartIndex () const
	Get the start index. Only valid if the XIC was processed separately.
int	getStartScanId () const
	Get the id of the start scan.
bool	getUseTimeShift () const
	Returns true if XIC are aligned based on time instead of scans.
bool	hasIndexes () const
	Return true if the functions that return indexes have valid data available to return.
Static Public Member Functions
static peakState	getCodeFromXml (std::string text)
	Get the status code for an XML attribute value.
static std::string	getXmlCode (peakState code)
	Get the XML attribute value for a status code.

Detailed Description

An eXtracted Ion Chromatogram (XIC).

This consists of a number of individual intensity values.

It also has start and end values and indices for the peaks, regions and the chromatogram itself

This is stored in XML in a "xic" entity.

Member Enumeration Documentation

enum peakState

Status codes from fitting peaks.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator:

PEAK_STATE_UNKNOWN	initial value
PEAK_STATE_OK	element is ok
PEAK_STATE_DISCARD	discard element from calc

Constructor & Destructor Documentation

ms_xic ( )

Default constructor.

Assigns reasonable default values to all internal members.

ms_xic ( const ms_xic_body & body ) [explicit]

Populated constructor. Performs a deep copy of the passed object.

Parameters:

body	The data loaded from the result file.

ms_xic ( ms_xic_body * body ) [explicit]

Constructor that use the same pointer as passed.

Parameters:

body	Is a pointer to existing data. The reference count for this will be incremented by this call.

Member Function Documentation

void defaultValues ( )

Use this member to re-initialise internal members.

Clears all values

ms_xic::peakState getCodeFromXml ( std::string text ) [static]

Get the status code for an XML attribute value.

Parameters:

text	The string used to encode the peak state in the XML file.

Returns:: The peak state corresponding to the XML encoded string.

double getElutionTimeShift ( ) const

Get the elution time shift in seconds.

Returns:: The value of the elution time shift.

int getEndIndex ( ) const

Get the end index. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is typically a zero based index of MS1 scans (either Survey or zoom) that have been 'filtered out' from all scan types

Returns:: Index at which the the XIC ends.

int getEndScanId ( ) const

Get the id of the end scan.

Returns:: The scan identifier at which the XIC ends.

int getNumPoints ( ) const

Get the number of points.

Returns:: The number of points in the XIC.

int getPeakEndIndex ( ) const

Get the end of the peak. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is a zero based index into the points array and should be 0..getNumPoints()

Returns:: Index at which the peak ends.

int getPeakEndScanId ( ) const

Get the index of the peak end.

Returns:: The scan identifier at which the peak ends.

int getPeakStartIndex ( ) const

Get the start of the peak. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is a zero based index into the points array and should be 0..getNumPoints()

Returns:: Index at which the peak starts.

int getPeakStartScanId ( ) const

Get the index of the peak start.

Returns:: The scan identifier at which the peak starts.

ms_xic::peakState getPeakState ( ) const

Get the state of the peak.

Returns:: The peak state.

void getPoint	(	int	index,
		double &	rt,
		int &	scanId,
		double &	intensity
	)		const

Get a point's values; retention time, scan number and intensity (index 1..n).

See Multiple return values in Perl, Java, Python and C#.

Parameters:

[in]	index	The index of the point to be queried (1..number of points).
[out]	rt	Filled with the retention time of the point.
[out]	scanId	Filled with the scan identifier of the point.
[out]	intensity	Filled with the intensity of the point.

int getRegionEndIndex ( ) const

Get the end of the region. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is a zero based index into the points array and should be 0..getNumPoints()

Returns:: Index at which the region ends.

int getRegionEndScanId ( ) const

Get the index of the region end.

Returns:: The scan identifier at which the region ends.

int getRegionStartIndex ( ) const

Get the start of the region. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is a zero based index into the points array and should be 0..getNumPoints()

Returns:: Index at which the region starts.

int getRegionStartScanId ( ) const

Get the index of the region start.

Returns:: The scan identifier at which the region starts.

double getRtPeakEnd ( ) const

Get the retention time of the peak end.

Returns:: The retention time of the peak end.

double getRtPeakStart ( ) const

Get the retention time of the peak start.

Returns:: The retention time of the peak start.

double getRtRegionEnd ( ) const

Get the retention time of the region end.

Returns:: The retention time of the region end.

double getRtRegionStart ( ) const

Get the retention time of the region start.

Returns:: The retention time of the region start.

int getStartIndex ( ) const

Get the start index. Only valid if the XIC was processed separately.

If loaded from XML this may be -1. XML version 1 does not store this information and considerable recalculate would be required to reproduce it.

The index is typically a zero based index of MS1 scans (either Survey or zoom) that have been 'filtered out' from all scan types

Returns:: Index at which the the XIC starts.

int getStartScanId ( ) const

Get the id of the start scan.

Returns:: The scan identifier at which the XIC starts.

bool getUseTimeShift ( ) const

Returns true if XIC are aligned based on time instead of scans.

Returns:: True if the elution time shift should be used.

std::string getXmlCode ( ms_xic::peakState code ) [static]

Get the XML attribute value for a status code.

Parameters:

code	The peak state to get the XML excoding string for.

Returns:: The string used to encode the peak state in the XML file.

bool hasIndexes ( ) const

Return true if the functions that return indexes have valid data available to return.

XML version 1 does not store this information and considerable recalculate would be required to reproduce it. And it's optional in the XML anyway.

Returns:: True if the XIC has all the index information, otherwise false.

The documentation for this class was generated from the following files:

ms_xic.hpp
ms_xic.cpp

ms_xic Class Reference [Quantitation analysis for Mascot Server and Distiller]

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

ms_xic Class Reference
[Quantitation analysis for Mascot Server and Distiller]